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Tuesday, April 6, 2021

SMRT Grant Winners – Collaboration Reaches New Heights in Global Science Challenge

Today we’re pleased to announce the three winners of our latest SMRT Grant which called for teams of researchers and collaborative projects that could be addressed using the power of HiFi sequencing. The winners are seeking to solve a diverse set of questions from mussel-hopping transmissible cancer to the power of pistachios to help tackle climate change, and sex determination in bearded dragons.     The 2020 HiFi for All – Collaborations SMRT Grant Program was open to scientists worldwide and offered three winning projects awards of up to 10 SMRT Cells 8M and sequencing on the Sequel II or…

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Thursday, March 4, 2021

Transcriptome Provides A Closer Look Into Giant Redwood Genome

Sequoia sempervirens is one of the tallest living trees on Earth, often reaching up to 300 ft It’s been a year since we took a little field trip to Stanford to collect samples from the giant California redwood (Sequoia sempervirens) with the goal of assembling its ginormous 27 Gb genome. What would have been considered a herculean effort not that many years ago was accomplished in only a few weeks by a handful of personnel —Emily Hatas (@EmilyHatas), Greg Young (@PacbioGreg), Michelle Vierra (@the_mvierra), and Greg Concepcion (@phototrophic) — in their spare time. As detailed in this blog post, the…

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Thursday, January 28, 2021

New Macaque Genome Provides a Big Boost for Biomedical Research

A high resolution reference genome for the rhesus macaque could help us better understand human disease. They may not be as well known as our chimpanzee or gorilla cousins, but macaques have played many key roles in scientific progress over the last half century. From launching into orbit during the early days of space travel to revealing the genetics of neurodevelopmental disorders and infectious diseases today, the rhesus macaque remains a key research primate around the world.   A new, comprehensively annotated reference genome unveiled last month boosts the potential of the most widely used non-human primate in biomedical research even…

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Tuesday, September 15, 2020

Now Available: Ultra-Low DNA Input Workflow for SMRT Sequencing

The SMRTbell gDNA Sample Amplification Kit enables whole genome amplification starting from as little as 5 ng of genomic DNA. It’s one of the questions we hear most often from scientists working with small organisms: Is it possible to generate truly high-quality, long-read data from minuscule amounts of DNA? With our new kit for ultra-low DNA input projects, the answer is: Absolutely!  The new workflow dramatically reduces the requirements for DNA quantity. Now, scientists need only 5 ng of genomic DNA to kick off a SMRT Sequencing project — that’s less than 2% of the starting volume needed for our…

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Wednesday, September 9, 2020

High Quality HiFi Assemblers Open Up a Wide New World of Genomics Possibilities

With PacBio HiFi sequencing data now readily available for organisms of any size, many exciting results have been published featuring new de novo assembly methods optimized for highly accurate long reads. These methods have produced assemblies for a variety of organisms at quality levels never before thought possible — as measured by completeness, contiguity and correctness. We feel privileged to collaborate with the scientific community on the development of these tools. From Small to Tall When the USDA wanted to rapidly assemble the Asian Giant Hornet as part of its real-time invasive species response initiative, they turned to a tool…

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Wednesday, August 26, 2020

Pangenome of Soybean Generated to Capture Genomic Diversity

A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. It has recently become apparent how important it is to sequence more than one individual to characterize the genomic variation within a species. This makes sense if you consider that sexually reproducing organisms are a mix of their parents and, therefore, not identical. This is just as true in crops as it is in humans. So, it’s not surprising that when a group of researchers from several institutions in China embarked on de novo genome assemblies of several accessions of…

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Wednesday, August 19, 2020

A TAL Tale: PacBio Sequencing Helps Unravel Mechanisms of Plant Infection

How do bacteria manipulate plant biology to cause blight and rot? Why are some pathogen strains more virulent than others? How can we engineer resistant staple food crops? These are pressing questions facing researchers looking to sustain and increase crop production against the backdrop of a changing environment.  For one major clade of pathogens, Xanthomonas spp, the answers lay locked within TAL effector genes (TALEs), but assembling these highly variable, repetitive regions was a long-standing obstacle. The key to finally unraveling the tangled assemblies was PacBio long-read sequencing.  Code-breaker Adam J. Bogdanove from Cornell University. Photo by Jesse Winter Plant…

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Thursday, August 6, 2020

“Murder Hornet” Genome Rapidly Assembled by USDA as Part of Real-Time Invasive Species Response Initiative

With a nickname like “murder hornet,” it’s no wonder the two-inch long Asian giant hornet (Vespa mandarinia) has caused a stir amongst those terrified of insect invasions.  Various species of paper wasp (left) compared to the Asian giant hornet (right) Photo by Hanna Royals, USDA. The wasps — which are actually more dangerous to bees than humans — have made another recent appearance in Washington state, and Agricultural Research Service (ARS) scientists are hoping a new rapidly-generated genome sequence of one of the insects will help in their quest to quash an invasion. Released August 6, the first high-quality genome…

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Wednesday, July 1, 2020

Don’t Sweat The Small Stuff: Low DNA Input Workflow Enables Sequencing of the Smallest Species

Tackling larger and larger genomes has been an attractive pursuit for many scientists as sequencing technologies improve at rapid rates. But what about the other end of the spectrum — the tiny organisms that comprise much of the diversity of life?  An obvious obstacle to decoding the DNA of small organisms such as insects, nematodes and other arthropods is collecting enough of it to actually sequence (usually multiple micrograms worth). Until recently, the solution was to pool DNA from many of these tiny creatures to create a representative sample, and extrapolate the biology of the individual constituents from there. But…

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Monday, March 16, 2020

A Menagerie of New Genomes Released by International Ensembl Project

The new and updated species in Ensembl 99 from the Vertebrate Genomes Project (VGP)   Meerkats, yaks, geese, and lots of flies — oh my! A full menagerie of new and updated animal genomes has been released by the Ensembl project.  The Ensembl 99 release includes a variety of vertebrates, plants, mosquitos, and flies, as well as updates of human gene annotation and variation data. Among them are 38 new species and two dog breeds (Great Dane and Basenji), as well as four updated genome assemblies. Many were created using PacBio sequencing data.    Thirteen of the new assemblies have…

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Thursday, January 23, 2020

Project to Rapidly Sequence Maize Pangenome Delivers Publicly Available Resource

Matt Hufford, associate professor at Iowa State University, helped produce a 26-line maize pangenome assembly collection Maize researchers have been rejoicing over a New Year’s gift delivered by a group of 33 scientists: A 26-line “pangenome” reference collection.  The multi-institutional consortium of researchers used the Sequel System and BioNano Genomics optical mapping to create the assemblies and high-confidence annotations. They released the results on January 9, and in several presentations at the Plant and Animal Genome XXVIII Conference, less than two years after the ambitious project was funded by a $2.8 million National Science Foundation grant.  The collection includes comprehensive,…

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Friday, December 27, 2019

SMRT Sequencing Highlights – Top Publications of 2019

With the release of the award-winning Sequel II System, 2019 was an exciting year for the SMRT Sequencing community. We were inspired by our users’ significant contributions to science across a wide range of disciplines. As the year draws to a close, we have taken this opportunity to reflect on the many achievements made by members of our community, from newly sequenced plant and animal species to human disease breakthroughs.   “It has been another phenomenal year for science. The introduction of the Sequel II System will accelerate discovery even more, and I can’t wait to see what 2020 will…

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Thursday, December 19, 2019

Release of Six New Reference-Quality Genomes Reveals Superpowers of Bats

Photo of a pale spear-nosed bat (Phyllostomus discolor) courtesy of the Rossiter Lab (@rossiterlab) Bat lovers and animal researchers have been waiting for insights into the evolution and remarkable genetic adaptations of our winged mammalian friends, ever since the global Bat1K initiative announced its quest to decode the genomes of all 1,300 species of bats using SMRT Sequencing and other technologies. Now, the first six reference-quality genomes have been released on the Hiller Lab Genome Browser, and described in a pre-print by Sonja Vernes (@Sonja_Vernes), Michael Hiller (@hillermich) and Gene Myers (@TheGeneMyers) of the Max Planck Institute, Emma Teeling (@EmmaTeeling1) of…

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Monday, November 11, 2019

Mapping the NLRome: Research Teams Turn to SMRT Sequencing to Trace Plant Immunity

There’s the genome, the transcriptome, the microbiome… and now the NLRome?  Breeders and pathologists have long been interested in uncovering the secrets of plant immunity, and much of their attention has been focused on receptors that can activate immune signalling: cell-surface proteins that recognize microbe-associated molecular patterns (MAMPs), and intracellular proteins that detect pathogen effectors, including nucleotide-binding leucine-rich repeat receptors (NLRs).  Hundreds of NLR genes can be found in the genomes of flowering plants. They are believed to form inflammasome-like structures, or resistosomes, that control cell death following pathogen recognition, and are being investigated as candidates for engineering new pathogen…

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Tuesday, November 5, 2019

Finding the Females: New Reference Genome Leads to Better Sex Determination Technique in Tuna

A team of Japanese researchers has used a new Pacific bluefin tuna reference genome to identify male-specific DNA markers in the fish The cultivation and conservation of one of the most important commercial fishes in the world may come down to sex determination — how can you successfully breed a species without knowing the sex of your stock? A Japanese research team has come up with a solution, thanks to a new Pacific bluefin tuna reference genome and the male-specific DNA markers they were able to identify as a result. In a study published recently in the Nature journal Scientific…

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